I once killed off the entire Dark brotherhood. A few days later, I, the Invincible Fierce Deity, started to notice the occasional citizen attacking me in public. People like Alvor, the companions newbloods Torvar, the dark elf, and Ria, and that guy who works for belethor attacked me on sight. Even Eorlund Gray-Mane, whom I befriended during the companions, and gave stormcloak buddies after kicking Balgruuf's ♥♥♥ from his throne, wanted me dead. Anyone care to try and tell me what is going on here?

No, that's just it. The only people I've killed are the ones who attacked me. The Dark Brotherhood, the Imperial Legion, and Madanach, the leader of the forsworn are the only people I've killed that didn't attack me.